dr inż. Agnieszka Lipska
Słowa kluczowe Pomoc
- molecular dynamics
- coarse grained models
- coarse graining, molecular dynamics, openmp, parallel algorithms, unres
- graphical processing unit
- high performance computing
- human norovirus
- protein folding
- protein structure prediction, multiscale modeling, unres force field, free and bioinformatics-assisted modeling, replica-exchange molecular dynamics
The UNited RESidue (UNRES) force field was tested in the 14th Community Wide Experiment on the Critical Assessment of Techniques for Protein Structure Prediction (CASP14), in which larger oligomeric and multimeric targets were present compared to previous editions. Three prediction modes were tested (i) ab initio (the UNRES group), (ii) contact-assisted (the UNRES- contact group), and (iii) template-assisted (the UNRES-template...
Optimization of parallel implementation of UNRES package for coarse‐grained simulations to treat large proteins
We report major algorithmic improvements of the UNRES package for physics-based coarse-grained simulations of proteins. These include (i) introduction of interaction lists to optimize computations, (ii) transforming the inertia matrix to a pentadiagonal form to reduce computing and memory requirements, (iii) removing explicit angles and dihedral angles from energy expressions and recoding the most time-consuming energy/force terms...
UNRES-GPU for Physics-Based Coarse-Grained Simulations of Protein Systems at Biological Time- and Size-Scales
The dynamics of the virus like particles (VLPs) corresponding to the GII.4 Houston, GII.2 SMV, and GI.1 Norwalk strains of human noroviruses (HuNoV) that cause gastroenteritis was investigated by means of long-time (about 30 μs in the laboratory timescale) molecular dynamics simulations with the coarse-grained UNRES force field. The main motion of VLP units turned out to be the bending at the junction between the P1 subdomain (that...
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